Website customer loyalty is believed to be very important to the success of E-Commerce firms. Based on document review, this study constructs a customer loyalty effect model which chooses organization, navigation, labeling and searching system as dependent variables as well as attitude and behavior loyalty as variables. The sample of the study was drawn from 250 students who have online shopping experience, 202 of usable questionnaires were included in the data analysis. Data analyses using correlation and regression analysis reveal that there was a strong and positive relationship between information architecture and customer loyalty. Also, organization, navigation, labeling and search systems were positively correlated with customer loyalty. The results could be a reference for designing of the E-Commerce website.